SMTL ID : 8tic.2 (1 other biounit)

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 11 residues within 4Å: Chain A: C.96, P.98, R.115, D.118, F.119, Y.122, Y.128, Y.213, R.214, T.216, N.219 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.128 Hydrogen bonds: A:D.118, A:R.214 NAG-NAG-BMA-MAN-MAN.2: 11 residues within 4Å: Chain B: C.96, R.115, D.118, F.119, Y.122, Y.128, Y.213, R.214, T.216, F.218, N.219 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.128 Hydrogen bonds: B:D.118, B:R.214

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: N.94, C.96, N.127, Y.128 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.128

2 x FKX: 3-(2-methylpropyl)-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxylic acid(Non-covalent)

FKX.4: 13 residues within 4Å: Chain A: K.149, S.150, L.151, H.154, D.215, T.216, F.217, L.220, K.223, D.245, D.246, K.288 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.151, A:F.217, A:F.217, A:D.245 Hydrogen bonds: A:D.215 Salt bridges: A:K.288 FKX.6: 13 residues within 4Å: Chain B: K.149, S.150, L.151, H.154, D.215, T.216, F.217, L.220, K.223, D.245, D.246, D.247, K.288 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.151, B:L.151, B:F.217, B:F.217, B:D.245 Hydrogen bonds: B:D.215 Salt bridges: B:K.288

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: L.151, H.154, R.157, D.247 Ligands: FKX.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.157, A:R.157, A:D.247

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain B: H.154, A.156, R.157 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jackson, J.J. et al., Imidazolone as an Amide Bioisostere in the Development of beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. J.Med.Chem. (2023)

Release Date

2023-12-06

Peptides

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2

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